Mass separators

ABSTRACT

In one implementation, processes for designing mass separators from a series of mass separator electric field data and processes for designing an ion trap from a range of data pairs and a mass analyzer scale are provided. Methods for producing mass separators including ion traps having Z 0 /r 0  ratios from about 0.84 to about 1.2 are also provided. Mass spectrometers are al provided that can include mass separators in tandem with one being an ion trap having a Z o /r o  ratio between 0.84 and 1.2. The present invention also provides methods for analyzing samples using mass separators having first and second sets of components defining a volume with a ratio of a distance from the center of the volume to a surface of the first component to a distance from the center of the volume to a surface of the second component being between 0.84 and 1.2.

CLAIM FOR PRIORITY

This application claims priority to U.S. provisional patent applicationSer. No. 60/430,223 filed Dec. 2, 2002, entitled “Optimized Geometry forIon Trap.”

RELATED PATENT DATA

This application is a 35 U.S.C. §371 of and claims priority to PCTInternational Application Number PCT/US03/38587, which was filed Dec. 2,2003 (02.12.03), and was published in English, which claims priorityunder 35 U.S.C. §119 to U.S. Provisional Patent Application No.60/430,223 which was filed Dec. 2, 2002 (02.12.02), the entirety of eachare incorporated herein by reference.

TECHNICAL FIELD

The present invention relates generally to the field of analyticaldetectors and more specifically to mass spectral ion detectors.

BACKGROUND OF THE INVENTION

Mass spectrometry is a widely applicable analytical tool capable ofproviding qualitative and quantitative information about the compositionof both inorganic and organic samples. Mass spectrometry can be used todetermine the structures of a wide variety of complex molecular species.This analytical technique can also be utilized to determine thestructure and composition of solid surfaces.

As early as 1920, the behavior of ions in magnetic fields was describedfor the purposes of determining the isotopic abundances of elements. Inthe 1960's, a theory describing fragmentation of molecular species wasdeveloped for the purpose of identifying structures of complexmolecules. In the 1970's, mass spectrometers and new ionizationtechniques were introduced which were capable of providing high-speedanalysis of complex mixtures and thereby enhancing the capacity forstructure determination.

It has become desirable to provide mass spectral analysis using portableor compact instruments. A continuing goal in designing these instrumentsis to optimize the components of the instrumentation.

SUMMARY OF THE INVENTION

According to one embodiment an ion trap is provided comprising a bodyhaving a length and an opening extending from a first end of the body toa second end of the body, the length having a center portion; a firstend cap adjacent to the first end of the body, the first end cap havinga surface proximate the first end and spaced a distance from the centerportion; a second end cap adjacent to the second end of the body, thesecond end cap having a surface proximate the second end and spaced thedistance from the center portion; and wherein the body and end capsdefine a volume between the surfaces of the first and second end capsand within the opening, the volume comprising the distance and a radiusof the opening, wherein the ratio of the radius to the distance is fromabout 0.84 to about 1.2.

An embodiment also provides a mass spectrometer comprising at least twomass separators in tandem, at least one of the two mass separatorscomprising an ion trap having a Z₀/r₀ ratio between 0.84 and 1.2.

Other embodiments are disclosed as is apparent from the followingdiscussion.

BRIEF DESCRIPTION OF THE DRAWINGS

Preferred embodiments of the invention are described below withreference to the following accompanying drawings.

FIG. 1 is a block diagram of a mass spectrometer according to anembodiment.

FIG. 2 is a cross-section of a Paul Ion Trap according to an embodiment.

FIG. 3 is an end view of the cross-section of the Paul ion trap of FIG.2 according to an embodiment.

FIG. 4 is a cross-section of a cylindrical ion trap according to anembodiment.

FIG. 5 is an end view of the cross-section of the cylindrical ion trapof FIG. 4.

FIG. 6 is a plot of octapole coefficient relative to quadrupolecoefficient as a function of Z₀/r₀ ratio for a CIT having an electrodespacing of 0.06 cm according to one embodiment.

FIG. 7 is a plot of quadrupole coefficient as a function of Z₀/r₀ ratiofor a CIT having an electrode spacing of 0.06 cm according to oneembodiment.

FIG. 8 is a plot of octapole and dodecapole coefficients relative toquadrupole coefficients as a function of electrode spacing for fiveZ₀/r₀ ratios according to one embodiment.

FIG. 9 is a comparison of simulation and experimental mass spectral dataacquired in accordance with one embodiment.

FIG. 10 is simulated mass spectral data acquired using a mass separatorhaving a Z₀/r₀=0.8.

FIG. 11 is simulated mass spectral data acquired using a mass separatorhaving a spacing of 2.56 mm.

FIG. 12 is simulated mass spectral data acquired in accordance with oneembodiment.

FIG. 13 is experimental mass spectral data acquired in accordance withone embodiment.

FIG. 14 is a comparison of the simulated data of FIG. 12 and theexperimental data of FIG. 13 according to an embodiment.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

At least some aspects provide processes for designing mass separatorsand ion traps, methods for producing mass separators and ion traps, massspectrometers, ion traps, and methods for analyzing samples.

Referring to FIG. 1, a block diagram of a mass spectrometry instrument10 is shown. Mass spectrometry instrument 10 includes a samplepreparation ionization section 14 configured to receive a sample 12 andconvey a prepared and/or ionized sample to a mass analyzer 16. Massanalyzer 16 can be configured to separate ionized samples for detectionby detector 18.

As depicted in FIG. 1, a sample 12 can be introduced into section 14.For purposes of this disclosure, sample 12 represents any chemicalcomposition including both inorganic and organic substances in solid,liquid and/or vapor form. Specific examples of sample 12 suitable foranalysis include volatile compounds such as, toluene or the specificexamples include highly-complex non-volatile protein based structuressuch as, bradykinin. In certain aspects, sample 12 can be a mixturecontaining more than one substance or in other aspects sample 12 can bea substantially pure substance. Analysis of sample 12 can be performedaccording to exemplary aspects described below.

Sample preparation ionization section 14 can include an inlet system(not shown) and an ion source (not shown). The inlet system canintroduce an amount of sample 12 into instrument 10. Depending uponsample 12, the inlet system may be configured to prepare sample 12 forionization. Types of inlet systems can include batch inlets, directprobe inlets, chromatographic inlets, and permeable or capillarymembrane inlets. The inlet system may include means for preparing sample12 for analysis in the gas, liquid and/or solid phase. In some aspects,the inlet system may be combined with the ion source.

The ion source can be configured to receive sample 12 and convertcomponents of sample 12 into analyte ions. This conversion can includethe bombardment of components of sample 12 with electrons, ions,molecules, and/or photons. This conversion can also be performed bythermal or electrical energy.

The ion source may utilize, for example, electron ionization (EI,typically suitable for the gas phase ionization), photo ionization (PI),chemical ionization, collisionally activated disassociation and/orelectrospray ionization (ESI). For example in PI, the photo energy canbe varied to vary the internal energy of the sample. Also, whenutilizing ESI, the sample can be energized under atmospheric pressureand potentials applied when transporting ions from atmospheric pressureinto the vacuum of the mass spectrometer can be varied to cause varyingdegrees of dissociation.

Analytes can proceed to mass analyzer 16. Mass analyzer 16 can includean ion transport gate (not shown), and a mass separator 17. The iontransport gate can contain a means for gating the analyte beam generatedby the ion source.

Mass separator 17 can include magnetic sectors, electrostatic sectors,and/or quadrupole filter sectors. More particularly, mass separators caninclude one or more of triple quadrupoles, quadrupole ion traps (Paul),cylindrical ion traps, linear ion traps, rectilinear ion traps (e.g.,ion cyclotron resonance, quadrupole ion trap/time-of-flight massspectrometers), or other structures.

Mass separator 17 can include tandem mass separators. In oneimplementation at least one of two tandem mass separators can be an iontrap. Tandem mass separators can be placed in series or parallel. In anexemplary implementation, tandem mass separators can receive ions fromthe same ion source. In an exemplary aspect the tandem mass separatorsmay have the same or different geometric parameters. The tandem massseparators may also receive analyte ions from the same or multiple ionsources.

Analytes may proceed to detector 18. Exemplary detectors includeelectron multipliers, Faraday cup collectors, photographic andstimulation-type detectors. The progression from analysis from inletsystem 3 to detector 7 can be controlled and monitored by a processingand control unit 20.

Acquisition and generation of data according to the present inventioncan be facilitated with processing and control unit 20. Processing andcontrol unit 20 can be a computer or mini-computer that is capable ofcontrolling the various elements of instrument 10. This control includesthe specific application of RF and DC voltages as described above andmay further include determining, storing and ultimately displaying massspectra, Processing and control unit 20 can contain data acquisition andsearching software. In one aspect such data acquisition and searchingsoftware can be configured to perform data acquisition and searchingthat includes the programmed acquisition of the total analyte countdescribed above. In another aspect, data acquisition and searchingparameters can include methods for correlating the amount of analytesgenerated to predetermined programs for acquiring data.

Exemplary ion traps are shown in FIG. 2-5. Referring to FIG. 2, a Paulion trap 30 is shown that includes a ring electrode 32 situated betweentwo end-cap electrodes 34. Trap 30 can have a toroidal configuration. Asshown in FIG. 3, a cross section of Paul ion trap 30 (e.g., hyperboliccross-section) shows ring electrode 32 and end caps 34. In thiscross-section, ring electrode 32 can be characterized as a set ofcomponents and end caps 34 can be characterized as a set of components.Ring electrode 32 includes an inner surface 36 and end caps 34 includean inner surface 38. Ring electrode 32 and end caps 34 define a volume40 having a center 42. Inner surface 36 is spaced a distance 46corresponding to half a distance intermediate opposing surfaces 36.Distance 46 can be referred to as r₀. Inner surface 38 is spaced adistance 48 half a distance intermediate opposing surfaces 38. Distance48 can be referred to as Z₀.

Referring to FIG. 4, a cylindrical ion trap (CIT) 50 is shown. CIT 50can include a ring electrode 52 having an opening 53. Configurations ofring electrode 52 other than the exemplary depicted ring structure arepossible. For example, ring electrode 52 can be formed as an opening abody of material having any exterior formation. Ring electrode 52 can besituated between two end-cap electrodes 54. In an exemplaryimplementation, electrode 52 can be centrally aligned between electrodes54.

In one implementation, electrodes 54 can be aligned over and opposingopening 53. Electrodes 54 can be flat and made of a solid materialhaving an aperture 56 therein. Stainless steel is an exemplary solidmaterial while other materials including non-conductive materials arecontemplated. Aperture 56 may be centrally located. Electrodes 54 caninclude multiple apertures 56. Individual electrodes 54 may also beconstructed either partially or wholly of a mesh. An exemplarycross-section of CIT 50 is shown in FIG. 5.

Referring to FIG. 5, ring electrode 52 includes an inner surface 58.Surface 58 can be substantially flat or uniform. End caps 54 have aninner surface 60. Surface 60 can be substantially flat or planar. Inthis cross-section ring electrode 52 can be characterized as a set ofcomponents and end caps 54 can be characterized as a set of components,each having surfaces 58 and 60 respectively. In an implementation,surfaces 58 oppose each other and surfaces 60 oppose each other.Surfaces 58 and surfaces 60 can also be orthogonally related. Ringelectrode 52 and end caps 54 define a volume 62 which may have a center64. In one implementation, openings 56 of end caps 54 can be alignedwith center 64. Inner surface 58 is spaced a distance 68 correspondingto half a distance intermediate opposing surfaces 58. Distance 68 can bereferred to as r₀ and the radius of opening 53. Inner surface 60 isspaced a distance 70 corresponding to half a distance intermediateopposing surfaces 60. Distance 70 can be referred to as Z₀. Electrode 52further includes a half height 72. CIT 50 can have electrode spacing 74between an end surface 76 of electrode 52 and surface 60. Spacing 74 canbe the difference between distance 70 and half height 72. In oneimplementation, half height 72 can be considered twice the length ofelectrode 52 with the center of the length being aligned with center 64.

Aspects are described below with respect of the embodiment of FIG. 5although it is to be understood that the below discussion is alsoapplicable to the embodiment of FIG. 3 or other constructions.Generally, analytes can be stored or trapped using mass separator 17such as an ion trap through the appropriate application ofradio-frequency (RF) and direct current (DC) voltages to the electrodes.For example, with respect to the embodiment of FIG. 5, and by way ofexample only RF voltage can be applied to ring electrode 52 with end capelectrodes 54 grounded. Ions created inside volume 62 or introduced intovolume 62 from an sample preparation ionization section 14, for example,can be stored or trapped in an oscillating potential well created involume 62 by application of the RF voltage.

In addition to storage, analytes can be separated using mass separator17 such as an ion trap. For example, and by way of example only, RF andDC voltages can be applied to electrodes 52, and 54 in such a way tocreate an electric field in volume 62 that trap a single (m/z) valueanalyte at a time. Voltages can then be stepped to the next m/z value,changing the electric field in volume 62, wherein analytes having thatvalue are trapped and analytes having the previous value are ejected toa detector. This analysis can continue step-wise to record a full massspectrum over a desired m/z range.

According to an exemplary aspect, the RF and DC voltages can be appliedto electrodes 52, 54 in such a way to create electric fields in volume62 trapping a range of m/z valued analytes simultaneously. The voltagesare then changed so that the trapped analytes eject from the ion trap toan external detector in an m/z dependent manner. For example, where noDC is applied and the RF amplitude is increased in a linear fashion,ions of increasing m/z can eject from the trap to a detector.Supplementary voltages may be applied during the RF amplitude ramp (orduring scans of other parameters such as RF frequency) to influence ionejection to the detector. For example, an alternating current (AC)voltage may be applied at the appropriate frequency to resonantly excitethe ions and cause their ejection in a process referred to as resonanceejection.

According to another implementation, the RF and DC voltages can beapplied to electrodes 52, 54 in such a way that a range of m/z valuesare trapped simultaneously or only a single m/z value is trapped. Theions are detected by their influence on some form of receiver circuit asthey undergo characteristic motion in volume 62. Exemplary receivercircuits include circuits that can receive an image current induced by acharged ion cloud on electrodes 52 and/or 54 or on a supplementaryelectrode and can measure the image current related to the m/z values ofthe ions.

Exemplary mass separators can be designed to provide optimum massanalysis performance including performance in the mass-selectiveinstability and resonance ejection modes of operation. According toexemplary implementations, an electric field of volume 62 can becontrolled by manipulation of mass separator geometry to increaseperformance. The mass separator geometry can include parameters such asZ₀, r₀, half height, and/or electrode spacing. The electric field caninclude a quadrupole field, higher order electric fields or otherfields. In exemplary implementations the quadrupole field and higherorder fields can be present in volume 62 and may influence analytemotion in volume 62 before and during mass analysis.

According to some embodiments, mass separator geometry parameters areselected to provide increased or optimum performance with respect to amass spectrometer. The discussion proceeds with respect to an initialmethod of providing mass separator electric field data. The massseparator electric field data includes data sets of mass separatorgeometric parameters and corresponding expansion coefficients. Accordingto one implementation a list of mass separator geometric parameters canbe generated (e.g., Z₀, r₀) and applied to Equations 1, 2, and/or 3below to generate the corresponding expansion coefficients therebycreating the data sets. In one aspect, a designer may select possiblevalues of the geometric parameters for application to the equation fordetermining corresponding coefficients. Other methods of generating thevalues of the geometric parameters are possible. According to anexemplary aspect the list is applied to equation 3 below.

An exemplary expression for the potential in an exemplary cylindricalion trap with no spacing 74 between ring end surface 76 and end-capelectrodes surface 60 and grounding the end cap electrodes 54 with RFvoltage applied to ring electrode 52 was developed by Hartung andAvedisian and is given in Equation 1:

$\begin{matrix}{{\Phi\left( {r,z} \right)} = {1 - {2{\sum\limits_{j = 1}^{\infty}\frac{\cosh\;\left( {x_{j}z} \right){J_{0}\left( {x_{j}r} \right)}}{x_{j}\cosh\;\left( {x_{j}z_{0}} \right){J_{1}\left( {x_{j}r_{0}} \right)}}}}}} & {{Equation}\mspace{14mu} 1}\end{matrix}$

In this expression, J₀ and J₁ are Bessel functions of the first kind,and x_(j)r₀ is the j^(th) zero of J₀(x). In one implementation, Equation1 may be expanded in spherical harmonics to yield Equation 2.

$\begin{matrix}{{\Phi\;\left( {r,z,\phi} \right)} = {A_{0} + {A_{1}z} + {A_{2}\left( {{\frac{1}{2}r^{2}} - z^{2}} \right)} + {A_{3}\left( {{\frac{3}{2}r^{2}z} - z^{3}} \right)} + {A_{4}\left( {{\frac{3}{8}r^{4}} - {3r^{2}z^{2}} + z^{4}} \right)} + \mspace{14mu}\ldots}} & {{Equation}\mspace{14mu} 2}\end{matrix}$

In an exemplary implementation, Equation 2 shows that the electric fieldin the described CIT may be considered as a superposition of electricfields of various order, or pole (“multipole expansion”). The expansioncoefficients for A_(n) where n=0–4 in Equation 2 correspond to themonopole, dipole, quadrupole, hexapole, and octapole componentsrespectively, and the relative magnitude of the coefficients candetermine the relative contribution of each field to the overallelectric field in the described CIT. According to one implementation,when only the coefficients for n=0 and n=2 are nonzero, the electricfield can be considered purely quadrupolar. The even orderedcoefficients can be calculated from Equation 3 of Kornienko et al.

$\begin{matrix}{A_{2n} = {\left\lbrack {{\frac{- 2}{{r_{0}^{2n}\left( {2n} \right)}!}{\sum\limits_{j = 1}^{\infty}\frac{\left( {x_{j}r_{0}} \right)^{{2n} - 1}}{\cosh\;\left( {x_{j}z_{0}} \right){J_{1}\left( {x_{j}r_{0}} \right)}}}} + \delta_{n,0}} \right\rbrack V_{ring}}} & {{Equation}\mspace{14mu} 3}\end{matrix}$

Here, δ_(n,0) is unity if n=0 and is otherwise zero.

According to another method of providing the mass separator electricfield data, the corresponding expansion coefficients can be generatednumerically from a list of provided geometric parameters using aPoisson/Superfish code maintained at Los Alamos National Laboratory (ThePoisson/Superfish code is available athttp://laacg1.lanl.gov/laacg/services/possup.html; see also, Billen, J.H. and L. M. Young. Poisson/Superfish of PC Compatibles, in Proceedingsof the 1993 Particle Accelerator Conference, 1993, Vol. 2 page 790–792;incorporated herein by reference) coupled with a CalcQuad/Multifitprogram available in the academic lab of Professor R. Graham Cooks,Purdue University, West Lafayette, Ind. In an exemplary implementationthe geometric parameters (e.g., Z₀, r₀) as well as a potential appliedto each component can be entered into a program utilizing thePoisson/Superfish code. The Poisson program can cover volume 62 withinthe specified geometric parameters with a mesh and then calculate apotential at each point on the mesh corresponding to the specificgeometric parameters and corresponding potentials applied to eachcomponent (e.g., Poisson electric field data). Harmonic analysis of thePoisson electric field data can then be carried out by inputting thePoisson electric field data into the CalcQuad/Multifit program to yieldthe expansion coefficients for each of the geometric parameters.

Exemplary data sets can include all of the coefficients (e.g., n=0–8)described above as well as the corresponding geometric parameters (e.g.,Z₀/r₀). In certain aspects the data sets can include octapole anddodecapole expansion coefficients.

In one embodiment, a range of geometric parameters are selected from thedata set that correspond to positive octapole coefficients and the leastnegative docecapole coefficients. For example, and by way of exampleonly, higher-order fields give large contributions to the overall fieldresulting in significant degradation of the performance of the massseparator in the mass selective instability mode, particularly if thehigher order coefficients are opposite in sign from the A₂ term. In oneimplementation this can be balanced by a small octapole superposition(A₈/A₂≦0.05), which has the same sign as the A₂ term (i.e., positive asshown in Equation 2), which may improve performance by off-settingeffects of electric field penetration into end-cap apertures 56 that maybe present to allow for entrance and egress of ions and/or ionizingagents such as electrons. Exemplary data pairs having this positiveoctapole coefficient, typically have a negative dodecapole (e.g.,≧−0.18, from 0 to −0.2, or ≧−0.05) coefficient. Data sets having largenegative dodecapole coefficients can have corresponding mass separatorgeometries that subtract from the overall electric field and hencedegrade trapping efficiency and mass separator performance. In anexemplary implementation, minimizing the dodecapole coefficient whileproviding adequate octapole coefficient can off-set the effect of thenegative dodecapole superposition to some extent. In another exemplaryimplementation, a larger percentage of positive octapole can optimizeCIT 50 performance. The exemplary use of the positive octapolecoefficient and the least negative dodecapole coefficient can provide aninitial range of ratios.

The range of ratios may be further refined in one example by identifyinga minimum and a maximum of the ratios for a given value of spacing 74.Referring to FIG. 6, a plot of octapole relative to quadrupolecoefficients (A₄/A₂) as a function of Z₀/r₀ using an exemplary spacingparameter of 0.06 cm illustrates that the Z₀/r₀ ratio should be greaterthan 0.84 to give positive octapole with a spacing of 0.06 cm betweenthe electrodes. Referring to FIG. 7, quadrupole (A₂) as a function ofZ₀/r₀ at an exemplary 0.06 cm spacing illustrates that as the Z₀/r₀ratio increases, the quadrupole field weakens requiring higher RFamplitude to achieve the same m/z analysis range. At Z₀/r₀˜1.2, roughlytwice the voltage would be needed to perform mass analysis over a givenrange than would be needed in an ideal trap (A₂=1). Accordingly, in oneembodiment a minimum Z₀/r₀ ratio of 0.84 and a maximum of 1.2 aredefined and may be used in geometries having spacing 74 other than 0.06cm.

At least one aspect also defines another geometric parameter in terms ofspacing 74 intermediate the electrodes. For example, an increase in thespace between electrodes (decrease of half-height) can be used tooptimize the field by minimizing the negative dodecapole coefficient.FIG. 8 demonstrates A_(n)/A₂ as a function of various Z₀/r₀ ratios. Asillustrated in FIG. 8, for each value of Z₀/r₀, as the spacing isincreased, a value of spacing 74 (also referred to as spacer value) isreached where the octapole coefficient A₄ crosses zero and becomesnegative. These spacer values at the zero crossings give a maximum valueof spacing 74 that can be used for a given Z₀/r₀. These spacer maximumvalues and corresponding Z₀/r₀ values in the range defined abovecorrespond to the respective zero-crossings in FIG. 8. Above a Z₀/r₀ratio of 1, the relationship between Z₀/r₀ and the spacer maximum valuesmay be essentially linear, with the spacer maximum values equal to1.2(Z₀/r₀)−0.77 cm.

An exemplary range of data pairs comprising Z₀/r₀ ratios and spacermaximum factors is shown in Table 1 below. The spacer maximum factors ofthe data pairs are usable to calculate spacer maximum values forrespective Z₀/r₀ ratios to ensure positive octapole superposition. Inone embodiment, the spacer maximum factors are scaled to yield thespacer maximum values. For example, a spacer maximum factor may bemultiplied by a scaling factor (e.g., r₀) to define the spacer maximumvalue for a respective ratio. The scaling factor can include scales theηm, μm, mm, or cm, for example. In the described example the spacermaximum factor is multiplied by r₀ to achieve scaling and determine theresultant spacer maximum value.

TABLE 1 Z₀/r₀ Spacer Maximum Factors 0.84 0.08 0.86 0.16 0.88 0.22 0.900.26 0.92 0.30 0.94 0.33 0.96 0.36 0.98 0.39 1.00 0.42 1.02 0.45 1.040.47 1.06 0.50 1.08 0.52 1.10 0.55 1.12 0.57 1.14 0.59 1.16 0.62 1.180.64 1.20 0.66

According to an embodiment, a mass separator may be produced by aligningthe first and second sets of components as shown and described in FIG. 5above with a ratio of Z₀ to r₀ of from about 0.84 to about 1.2. In oneexample, a desired r₀ and Z₀/r₀ ratio may be chosen based upon designcriteria (e.g., available RF power supply, gas-tightness, gasthroughput, minimization of gas pumping). Z₀ is determined from theselected r₀ and ratio. The spacing 74 is determined from the maximumspacer factor times the scaling factor (e.g., r₀). The utilized spacing74 may be equal to or less than the maximum spacer factor times r₀ inone embodiment.

Instrument 10 can be calibrated with a known composition such asperfluorotri-n-butylamine (pftba) or perfluorokerosene. Once calibrated,the instrument can provide mass spectra of analytes produced accordingto the methods described above.

Simulation of instruments 10 designed in accordance with disclosedaspects versus other designs is provided below. The results of thesimulations are provided in FIGS. 9–12 and 14.

Mass spectral data simulations were performed using an ITSIM 5.1 programavailable from the laboratory of Prof. R. Graham Cooks at PurdueUniversity. (Bui, H. A.; Cooks, R. G. Windows Version of the Ton TrapSimulation Program ITSIM: A Powerful Heuristic and Predictive Tool InIon Trap Mass Spectrometry J. Mass Spectrom. 1998, 33, 297–304, hereinincorporated by reference). The ITSIM program allows for the calculationof trajectories (motion paths) of ions stored in ion trap massspectrometers, including cylindrical ion traps (CITs). The motion ofmany thousands of ions can be simulated, to allow for a statisticallyvalid, realistic comparison of the simulated ion behavior with the datathat are obtained experimentally. Full control of experimentalvariables, including the frequency and amplitude of the RF trappingvoltage and the frequencies and amplitudes of additional waveformsapplied to the ion trap end caps is provided by the simulation program.A collisional model that allows for simulation of the effects ofbackground neutral molecules present in the ion trap that may collidewith the ions is also provided. To perform a simulation, the followingsteps may be performed: 1) the characteristics (e.g. mass, charge, etc.)of the ions to be simulated are specified, 2) the characteristics of theion trap (e.g. size) are specified, 3) the characteristics of theexperiment to be simulated (e.g. voltages applied to the CIT) arespecified, and 4) the motion of the ions under these conditions arecalculated using numerical integration. In the sections that follow,exemplary details for each of these steps is given.

1) The Ions

Three ensembles of ions were created to simulate the ions generated viaelectron ionization of toluene (C₇H₈). The ions were generated randomlyin time during the first three microseconds of the simulation, with thecharacteristics detailed in Table 2:

TABLE 2 Characteristics of ions in simulation data Ion Ensemble 1 IonEnsemble 2 Ion Ensemble 3 mass 65 Da 91 Da 92 Da (m) Charge 1 1 1 (z)Number 250 1500 750 of ions initial 0 ± 0.3 mm, 0 ± 0.3 mm, 0 ± 0.3 mm,radial initial 0 ± 0.15 mm, 0 ± 0.15 mm, 0 ± 0.15 mm, axial initial 0m/sec. 0 m/sec. 0 m/sec. veloc- ity

2) The Cylindrical Ion Traps

To yield the most accurate comparison between the simulation and theexperiment, the cylindrical ion traps used in the simulations describedhere were defined by calculating an array of potential values for thespecific CIT geometry under study. This method allows for the effects ofeach geometry detail, such as electrode spacing and end-cap hole size,to be most accurately represented. To achieve this using the ITSIMprogram, the geometric coordinates for each electrode of the trap arespecified as x,y pairs in a text file, together with the potentialapplied to each electrode. This file can then be loaded into a CreatePotprogram (available from the laboratory of Professor R. Graham Cooks,Purdue University, West Lafayette, Ind., and based on thePoisson/Superfish code described above) that calculates the potential ateach point on a rectangular grid within the ion trap volume, and thisarray of potential points is then loaded into memory for use in the iontrajectory calculation. For the simulations described here, a grid ofapproximately 100,000 points was used to represent the potentialdistribution in the CIT. Before the start of a simulation, thecomponents of the electric field vector are obtained by taking thederivative of the potentials on the grid points using centereddifferencing. During the simulation, the electric field is determined ateach time step for each ion position by bilinear interpolation from theelectric field components on the adjacent grid points.

For the simulation data shown below, each aspect of the CIT geometry waskept constant except for the parameter under test. Potential array fileswere generated for each geometry and used to simulate the trajectoriesof the same ensembles of ions, as defined above, using the samesimulation conditions defined below. In this way, the effects of thegeometry change on the ion motion, and ultimately on the mass spectrum,could be measured.

3) The Characteristics of the Experiment Simulated

An ion trap experiment is defined by the voltages applied to theelectrodes of the trap, and how those voltages vary as a function oftime. For the simulations performed here, the voltages were applied intwo segments, with a total simulation length of 5.13 ms. The details ofthe voltages applied during each segment are given in Table 3.

TABLE 3 Segment 1 (0.5 ms Segment 2 (4.63 ms Electrode duration)duration) Ring Sine Sine Freq: 1.5 MHz Freq: 1.5 MHz Amp: constant toyield trap Amp: ramped from low-mass cutoff (LMCO) = LMCO 50 to LMCO 10050 (actual voltage amplitude (actual voltage varied with geometry suchvaried, scan rate that lowest mass trapped at was always 10.8 Da/ms)q_(z) = 0.64 was always m/z 50) End Caps no voltage applied Sine Freq:375 kHz Amp: ramped from 1.84 V to 3.41 V (chosen to match experiment)

Segment 1 is a 0.5 ms stabilization time, to allow the ions to come toequilibrium with the background gas through collisions. Segment 2 is amass analysis ramp using the mass selective instability mode withresonance ejection. The trapping voltage on the ring electrode is rampedin amplitude during this segment to bring ions to resonance with thevoltage applied to the end caps, in order of m/z ratio. When the ionsreach the resonance point, they are excited by the voltage on the endcaps and are ejected from the trap.

The simulations performed here included the effects of background gaspresent in the ion trap. The gas was assumed to be mass 28 (e.g.nitrogen to simulate an air background) at a temperature of 300 K and apressure of 6×10⁻⁵ Torr, to match the experiments. At each time step ofthe simulation, a buffer gas atom is assigned a random velocitygenerated from a Maxwell-Boltzmann distribution. A random number from auniform distribution is then compared to the collision probability todetermine if a collision occurs. The collision probability is calculatedassuming a Langevin collision cross section, with the hard-sphere radiusof the ions equal to 50 Å² and the polarizability of the neutral gasequal to 0.205 Å³. The simulation assumes that the gas velocity israndomly distributed, and also assumes that any scattering of the iontrajectories that may occur is in a random direction. Only elasticcollisions are considered, i.e. only kinetic energy, but not internalenergy, is transferred during the collision.

4) Calculation of Ion Motion

ITSIM calculates the trajectories of each ion in the ensemble bynumerically integrating the equation of motion under the conditionsspecified above. When an ion leaves the ion trap volume, or at the endof the simulation, the location of each ion, and the time it has leftthe trap if applicable, is recorded. For the simulations performed here,the integration was performed using a fourth-order Runge-Kutta algorithmwith a base time step size of 10 ns. The voltages applied to the trapswere varied as described above, and the location of each ion in the trapwas calculated every 10 ns. For the simulations performed here, most ofthe ions had ejected from the trap through the end-cap holes, and hencewere recorded to have left the trap and struck a “detector” placed justoutside the trapping volume.

In the mass-selective instability with resonance ejection mode ofoperation which is simulated here, ions are ejected from the ion trap inorder from lowest to highest m/z ratio, as described above. By plottingthe ejection time of the ions as a function of ion number, a massspectrum of the ions can be generated. The simulated data for ion numberat the detector vs. ejection time were exported to Excel for plottingand calibration to generate the mass spectra given in the figures below.

Experimental data was also obtained from exemplary instruments 10fabricated according to aspects of the disclosure. Experimental resultsare shown in FIGS. 9, 13, and 14.

Experimental Details

The experimental data given in the figures below was generated on aGriffin Analytical Technologies, Inc. Minotaur Model 2001A CIT massspectrometer. (Griffin Analytical Technologies, West Lafayette, Ind.(Griffin)). The CIT used in the Griffin mass spectrometer to record thedata presented below has a ring electrode radius, r₀ of 4.0 mm, acenter-to-end cap spacing, Z₀ of 4.6 mm, and a ring-to-end cap spacingof 1.28 mm. The CIT, along with the electron generating filament and thelenses used to transport the electrons to the CIT for ionization, arehoused in a vacuum chamber that is pumped by a Varian V7OLPturbomolecular pump, backed by a KNF Neuberger 813.5 diaphragm pump. Thepressure inside this chamber can be set using a Granville-Phillips Model203 variable leak valve; for the data collected here, the chamberpressure was set to 6×10⁻⁵ Torr of ambient room air, as measured on aGranville-Phillips 354 Micro-Ion® vacuum gauge module.

With this instrument, volatile gas-phase samples are introduced into thevacuum chamber via a polydimethylsiloxane (PDMS) capillary membranelocated inside the chamber. Organic compounds, such as toluene, aredrawn through the inside of the membrane, permeate into the membranematerial, and then desorb from the outside surface of the membrane intothe vacuum chamber. The main constituents of air, such as oxygen andnitrogen, are rejected by the membrane and hence do not enter the vacuumchamber. The analyte molecules that enter the vacuum chamber are ionizedinside the CIT by an electron beam that is generated from a heatedfilament and is then directed into the trap with a set of three lenses.The trapped ions are allowed to cool via collisions with background air,and are then scanned from the trap to an external detector in themass-selective instability with resonance ejection mode as describedabove.

Toluene was introduced to the instrument by drawing the headspace vaporsof the neat liquid through a one centimeter PDMS membrane at a flow rateof approximately 2 L/min using a KNF Neuberger MPU937 diaphragm pump.The membrane was at ambient temperature. The toluene molecules wereionized in the CIT for 50 ms with the 1.5 MHz trapping RF set to avoltage that corresponded to a LMCO in the trap of m/z 50 (note that forthe Griffin CIT, the LMCO values are specified for q_(z)=0.64, notq_(z)=0.908 as is typical for most standard ion traps). The ions werethen allowed to cool for 25 ms at LMCO 50 before mass analysis. For massanalysis, the RF on the ring electrode was ramped from a LMCO of 50 to aLMCO of 150, at a scan rate of 10.7 Da/ms. During mass analysis, the endcap sine voltage of 375 kHz was ramped in amplitude from a startingvalue of 0.95 V to 1.85 V. Note that the end caps are connected in sucha way that when one end cap has a positive voltage applied, the otherhas a corresponding negative voltage applied, so that the potentialbetween the end caps is actually twice the amplitude of the voltageapplied between each end cap and ground. This accounts for thefactor-of-two difference in the end cap voltage specified here in theexperimental section and that specified above in the simulations. Theions were detected with a combination conversion dynode/electronmultiplier detector. The dynode was held at −4 kV, and the electronmultiplier at −1.2 kV.

Simulation and Experimental Data

FIG. 9 is a comparison of simulated and experimental mass spectra forperfluoro tributalamine (PFTBA) collected under identical conditionsusing a cylindrical ion trap with Z₀=4.6 mm, r₀=4.0 mm (Z₀/r₀=1.15), andelectrode spacing=1.28 mm.

FIG. 10 is a simulated mass spectrum of toluene calculated for acylindrical ion trap with Z₀=3.2 mm, r₀=4.0 mm (Z₀/r₀=0.8), andspacing=0.6 mm, illustrating that when the condition 0.84 is not met,the mass spectral performance of the CIT is poor; i.e. the peaks arebroadened and are not well-resolved.

FIG. 11 is a simulated mass spectrum of toluene calculated for acylindrical ion trap with Z₀=4.6 mm, r₀=4.0 mm (Z₀/r₀=1.15), andspacing=2.56 mm, illustrating that when the spacer is greater than thatdefined in Table 1 for this value of Z₀/r₀ the mass spectral performanceis poor; i.e. the peaks are broadened and are not well-resolved.

FIG. 12 is a simulated mass spectrum of toluene calculated for acylindrical ion trap with Z₀=4.6 mm, r₀=4.0 mm (Z₀/r₀=1.15), andspacing=1.28 mm, illustrating that when the spacer is within the rangedefined in Table 1 for this value of Z₀/r₀, the mass spectralperformance is improved; i.e. the peaks are narrower and more defined,and the signals for ions of m/z 91 and m/z 92 are well-resolved.

FIG. 13 in an experimental mass spectrum of toluene obtained on theGriffin mass spectrometer using a cylindrical ion trap with Z₀=4.6 mm,r₀=4.0 mm (Z₀/r₀=1.15), and spacing=1.28 mm, illustrating that, when theCIT is constructed according to the geometry specifications definedabove, the mass spectral performance is improved.

FIG. 14 is a comparison of the simulated and experimental data fromFIGS. 12 and 13.

The invention has been described in language more or less specific as tostructural and methodical features. It is to be understood, however,that the invention is not limited to the specific features shown anddescribed, since the means herein disclosed comprise preferred forms ofputting the invention into effect. The invention is, therefore, claimedin any of its forms or modifications within the proper scope of theappended claims appropriately interpreted in accordance with equitabledoctrines.

In compliance with the statute, the invention has been described inlanguage more or less specific as to structural and methodical features.It is to be understood, however, that the invention is not limited tothe specific features shown and described, since the means hereindisclosed comprise preferred forms of putting the invention into effect.The invention is, therefore, claimed in any of its forms ormodifications within the proper scope of the appended claimsappropriately interpreted in accordance with the doctrine ofequivalents.

1. A mass separator comprising: first and second sets of electrodecomponents, individual ones of the components comprising a surface,wherein, in a cross section, the surfaces of the first set of componentsoppose each other, the surfaces of the second set of components opposeeach other, and the surfaces of the first and second sets of componentsdefine a volume, the volume comprising a first distance corresponding toa half a distance intermediate opposing surfaces of the first ofcomponents and a second distance corresponding to a half a distanceintermediate opposing surfaces of the second set of components, wherein,a ratio of the first distance to the second distance comprises fromabout 0.84 to about 1.2; and wherein the mass separator comprises acylindrical ion trap and the surface of the first component comprisesthe surface of at least one of the end caps of the ion trap and thesurface of the second component comprises the inner surface of the ringelectrode of the ion trap, the cylindrical ion trap comprising anelectrode spacing distance between individual ones of the end caps andthe ring electrode, wherein the electrode spacing distance is related tothe ratio by a spacer maximum factor and the electrode spacing distanceis less than the product of the spacer maximum factor times the seconddistance.
 2. The mass separator of claim 1 wherein the end caps comprisestainless steel mesh.
 3. The mass separator of claim 1 wherein the firstset of components are orthogonally related to the second set ofcomponents.
 4. The mass separator of claim 1 wherein at least one of theend caps comprises a solid material having a centrally located aperture.5. The mass separator of claim 1 wherein at least one of the end capscomprises mesh.
 6. The mass separator of claim 1 wherein at least one ofthe end caps further comprises an opening.
 7. The mass separator ofclaim 6 wherein the opening is aligned with the volume center.
 8. Themass separator of claim 1 wherein the mass separator is coupled to amass detector.